Sequence
atgc intronic sequence ATGC exonic sequencegtatttccggtcaaccagttttcttatattttaaggattttgatttctatcaccttatcgattatggtttcgatgatttcagATCGAAATGTTATCCAAGATAAACCACAAGAATTTTGTCAACCTTCTTGGTTACTGTGAAGAAGAAGAACCTTTCACTAGGATCTTGGTCTTTGAATATG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G56050.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G56050.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os05g39410.1 (Oryza sativa), 3'ss of exon 7
--gtatttccggtcaaccagttttcttatattttaaggattttgatttctatcaccttat-cgattatggtttcgatgatttcagATCGAAATGTTATCCAAGATAAACCACAAGAATTTTGTCAACCTTCTTGGTTACTGTGAAGAAGAAGAACCTTTCACTAGGATCTTGGTCTTTGAATATG
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gtatataatggttttttctgtattatttcttccgcagggaa--gatgtttacttactaacatggatatgctat-ggtg-ttctagGTTGAAGTCTTATCAAAAGTGAGCCATAAGAATTTAATGAACCTTGTGGGTTACTGTGAAGATGAAGAACCATTCACTCGGATGATGGTGTTTGAGTATG
upper sequence: AT3G56050.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G43150.1 (Glycine max), 3'ss of exon 8
--------------------------gtatttccggtcaaccagttttcttatattttaaggattttgatttctatcaccttatcgattatggtttcgatgatttcagATCGAAATGTTATCCAAGATAAACCACAAGAATTTTGTCAACCTTCTTGGTTACTGTGAAGAAGAAGAACCTTTCACTAGGATCTTGGTCTTTGAATATG
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gtacaccaattattataacagaaaaaacccagcaaatttaactgtagaattgcaattcaggaaatttaattataactaacttcttaaccata----ccatggcttcagATAGATACATTGTCGAAAGTGAACCACAAGAATTTTGTCAATCTTATTGGATACTGTGAAGAAGAGGATCCTTTCACCAGAGTGTTGGTTTTTGAATATG
upper sequence: AT3G56050.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA14G06230.1 (Glycine max), 3'ss of exon 7
-----------------------------------gtatttccggtcaaccagttttcttatattttaaggattttgatttctatcaccttatcgattatggtttcgatgatttcagATCGAAATGTTATCCAAGATAAACCACAAGAATTTTGTCAACCTTCTTGGTTACTGTGAAGAAGAAGAACCTTTCACTAGGATCTTGGTCTTTGAATATG
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gtacgtcaattatcataacagaaaagaaaaaaaaaacccagcaaatttaactgtagaattgcaatttaggaaatttgattattactaacttcttaaccatc------atggtttcagATAGATAAATTGTCGAAAGTGAACCACAAGAATTTTGTGAATCTTATTGGATACTGTGAAGAAGAGGAGCCTTTCACCAGAATGTTGGTTTTTGAATATG
upper sequence: AT3G56050.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G02850.1 (Glycine max), 3'ss of exon 7
gtatttccggtcaaccagttttct-tatattttaaggattttgatttctatcaccttatcgattatggtttcga-------tgatttcagATCGAAATGTTATCCAAGATAAACCACAAGAATTTTGTCAACCTTCTTGGTTACTGTGAAGAAGAAGAACCTTTCACTAGGATCTTGGTCTTTGAATATG
||| | || || | | | | |||| |||||| | | | | | || ||| | || |||||||| || | ||||| || | ||||||||||||||||| || |||||||| | ||||||||||| || |||||||| || || |||| ||||| ||||
gtactgccaactaaaacataaacaatttcttttttagattttcaactaggctgctattgtaactaacattttaagcaattatggtttcagATAGATACATTATCAAAAGTGAACCACAAGAATTTTGTAAATCTTCTTGGACATTGTGAAGAAGATGAGCCTTTCACCAGAATGGTGGTTTTTGAGTATG
upper sequence: AT3G56050.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G35570.1 (Glycine max), 3'ss of exon 6
gtatttccggtcaac---cagttttcttatattttaaggattttgatttctatcaccttatcgattatggtttcga-------tgatttcagATCGAAATGTTATCCAAGATAAACCACAAGAATTTTGTCAACCTTCTTGGTTACTGTGAAGAAGAAGAACCTTTCACTAGGATCTTGGTCTTTGAATATG
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gtactaccacctaaaacataaacatttatttttttgtagatttccaattaggctgctattgtaactaatattttaagcaattatgatttcagATAGATACATTATCAAAAGTGAACCACAAGAATTTTGTAAATCTTCTTGGACATTGTGAAGAAGATGAGCCTTTCACCAGAATGGTGGTTTTTGAGTATG
upper sequence: AT3G56050.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv13s0067g01550.t01 (Vitis vinifera), 3'ss of exon 7
gtatttccggtcaaccagttttcttatattttaaggattt---tgatttctatcaccttatcgattatggtttcgatgatttcagATCGAAATGTTATCCAAGATAAACCACAAGAATTTTGTCAACCTTCTTGGTTACTGTGAAGAAGAAGAACCTTTCACTAGGATCTTGGTCTTTGAATATG
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gtactt--gagagattacatccactaaactttgtggttttgattcatcttggtagtccttacattttctttggttgtggtttcagATCGAAAGGTTATCAAAAGTGAACCACAAGAATTTTGTCAACCTTCTCGGATATTGTGAAGAAGAGGAACCTTTCACCAGAATGATGGTTTTTGAATATGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|86054312|gb|DR350069.1|DR350069EST: CGTCTGCCAAAGAATGGACAAATAACATAGAAATGCAGTTCAGAAAGAAG ATCGAAATGTTATCCAAGATAAACCACAAGAATTTTGTCAACCTTCTTGGT
genomic: CGTCTGCCAAAGAATGGACAAATAATATAGAAATGCAGTTCAGAAAGAAGgtatttccgg ... atgatttcagATCGAAATGTTATCCAAGATAAACCACAAGAATTTTGTCAACCTTCTTGGT
EST:
gi|86054311|gb|DR350068.1|DR350068EST: CGTCTGCCAAAGAATGGACAAATAACATAGAAATGCAGTTCAGAAAGAAG ATCGAAATGTTATCCAAGATAAACCACAAGAATTTTGTCAACCTTCTTGGT
genomic: CGTCTGCCAAAGAATGGACAAATAATATAGAAATGCAGTTCAGAAAGAAGgtatttccgg ... atgatttcagATCGAAATGTTATCCAAGATAAACCACAAGAATTTTGTCAACCTTCTTGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttaaggattttgatttctatcaccttatcgattatggtttcgatgatttcagATCGAAATGTTATCCAAGATAAACCACAAGAATTTTGTCAACCTTCTTGGTTACTGTGAAGAAGAAGAACCTTTCACTAGGATCTTGGTCTTTGAATATG
ttttgat putative branch site (score: 4)
attttgatttctat TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttccggtcaaccagttttcttatattttaaggattttgatttctatcaccttatcgattatggtttcgatgatttcagATCGAAATGTTATCCAAGATAAACCACAAGAATTTTGTCAACCTTCTTGGTTACTGTGAAGAAGAAGAACCTTTCACTAGGATCTTGGTCTTTGAATATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC